title: n=3/2percent/empty

city: Kyoto

first: Hiromi

last: Ii

state: Kyoto

address: 5 Nakauchi-cho, Misasagi, Yamashina-ku,

institute: Kyoto Pharmaceutical University

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100percent).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2percent of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: NIH3T3 fibroblast cell line

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The mouse fibroblast NIH3T3 cell line was purchased from American Type Culture Collection (Rockville, MD). The cells were cultured in DMEM supplemented with 2percent FBS (HyClone, South Logan, UT) and 1percent penicillin and streptomycin (Wako Pure Chemical Industries, Osaka, Japan) and maintained at 37 ºC in 5percent CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells lysed with Trizol (Thermo Fisher Scientific, Waltham, MA) and purified with the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Stably GGCT-expressing NIH3T3 cells were established via retroviral infection with pCX4bsr vector. NIH3T3 cells were transfected with GGCT expression retroviral vector or control vector.


title: n=3/2percent/GGCT-OE

status: Public on May 20 2024

type: RNA

country: Japan

molecule: total RNA

organism: Mus musculus

tag: cell line


title: n=2/2percent/empty


title: n=1/2percent/GGCT-OE


title: n=1/2percent/empty


title: WK-521_Hilum_2dpi_2

type: SRA

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

institute: The Institute of Medical Science, The University of Tokyo

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed with fastp (v.0.21.0).
Sequenced reads were mapped to the golden hamster, SARS-CoV-2, and BANAL-20-236 reference genomes using STAR (v.2.6.1c).
Assembly: Golden hamster (GCF_017639785.1), BANAL-20-236 (MZ937003.2), and SARS-CoV-2 (NC_045512.2)
Supplementary files format and content: Expression read count matrix of hamster lung hila and peripheries (out_featureCount_matrix.txt)

organism: Mesocricetus auratus

source_name: lung hilum

extract_protocol:
Total RNA was extracted using QIAamp RNA Blood Mini Kit (Qiagen, Cat# 52304)
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

tag: tissue

value: lung hilum

tag: infection

tag: time


title: MAC-T cells, IL10Rα knockout, no infection, rep4 (KO_12)

city: Guelph

first: Christine

middle: Francoise

last: Baes

state: Ontario

address: 50 Stone Road East

department: Animal Biosciences

country: Canada

institute: University of Guelph

data_processing:
CLC Genomics Workbench software 20.0.4 (QIAGEN, Aarhus, Denmark)
The sequence data were trimmed for adaptor sequence, low-quality sequence (Phred score >30) using CLC genomic benchwork (parameter- Quality limit: 0.05 and max 2 ambiguous nucleotides)
The trimmed pair-end sequence reads were mapped to the bovine reference genome (ARS-UCD1.2) using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.6 similarity fraction: 0.6)
Differentially expressed (DE) genes analyses for "MAC-T cells, wildtype, no infection" versus "MAC-T cells, wildtype, MAP infection", "MAC-T cells, wildtype, no infection" versus "MAC-T cells, IL10Rα knockout, no infection", "MAC-T cells, wildtype, MAP infection" versus "MAC-T cells, IL10Rα knockout, MAP infection", and "MAC-T cells, IL10Rα knockout, no infection" versus "MAC-T cells, IL10Rα knockout, MAP infection" contrasts were performed
Gene expression levels were quantified in reads per kilobase per million mapped reads (RPKM) and transformed to log 2 were performed using CLC genomic benchwork
DE genes between each contrast were defined by a p-value ≤0.01, FDR ≤0.05, and |fold change|≥2.
Assembly: Bos taurus ARS-UCD1.2
Supplementary files format and content: Common delimited text files.  Chromosome, start and end physical position, fold change, p-value, FDR p-value correction, gene, Ensemble ID, and RPKM (reads per kilobase of transcript, per million mapped reads) for each of the samples being included in the contrast.

organism: Bos taurus

source_name: mammary epithelium

growth_protocol:
MAC-T wild type and IL10RA KO cell line were cultured in T25 tissue culture flasks (Corning, Tewksbury, MA, USA) at 37 °C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM; Invitrogen, Burlington, ON, Canada) supplemented with 4.0 mM L-glutamine, 10% heat inactivated fetal bovine serum (FBS; Invitrogen), 25 mM HEPES buffer (Invitrogen), 0.25 μg/ml amphotericin B (Invitrogen), 1% Penicillin/Streptomycin (100 unit/ml of Penicillin and 100 μg/ml Streptomycin; Invitrogen), 1 mM Sodium Pyruvate (Invitrogen), and 5 μg/ml insulin-transferrin-selenium (Invitrogen).
Mycobacterium avium subsp. Paratuberculosis (MAP) was cultured in Middlebrook 7H9 broth (Sigma-Aldrich) supplemented with 10% oleic acid, albumin, dextrose, catalase (OADC; Becton, Dickinson, Canada), 0.05% Tween 80 (Sigma-Aldrich), and 2 mg/L mycobactin J (Allied Monitor Inc., Fayette, MO). The bacterial culture was incubated at 37°C and 5% CO2.

extract_protocol:
Total RNA extraction was carried out using the RNeasy mini kit (Qiagen, Germany) from both uninfected and MAP-infected samples according to the manufacturer’s protocol. The DNA traces were removed by DNase I treatment (Fermentas, Waltham, MA, USA). The concentration and purity of the RNA samples were determined at A260/280 nm ratios using the Cytation-5 Spectrophotometer. The integrity of the RNA samples was assessed using Bioanalyzer. The samples with higher than 7 RNA Integrity Number (RIN) were chosen for RNA Seq.
RNA-seq, including library construction were outsourced to Genewiz, Azenta Life Sciences, US

treatment_protocol: The IL10RA KO and Wild type MAC-T cells were seeded at 1.2 x10^5 cells per well in separate 24-well plates and incubated overnight at 37°C and 5% CO2 to reach 80% confluence. Both cell types were either infected with MAP or provided an equivalent volume of MAP-carrier solution media (uninfected control) for 72 h. Bacterial CFU were determined using the pellet wet-weight method, whereby 1 mg of MAP Madonna pellet was equal to 10^7 CFU. MAP was added to each cell type to achieve a 10:1 multiplicity of infection and then spun for 2 min at 250x g to ensure MAP interaction with the cells.

value: mammary epithelium

tag: genotype

value: IL10R{alpha} knockout

tag: treatment

value: No treatment


title: LKR13-KK-1

city: Houston

first: Yu

last: Qian

address: 1515 Holcombe blvd

country: USA

institute: MDACC

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw scRNA-seq data were preprocessed using the Cell Ranger pipeline analysis provided by 10×Genomics. After data filtering, doublets removal, batch-effect evaluation and data normalization as described previously, “Seurat” R package (v3.1.5) was used to analyze the normalized gene-cell matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous tumor

extract_protocol:
Tumors were harvested and dissociated in single cell suspension accroding to the protocol. Briefly, tumor tissues were mechanically disrupted and digested with Collagenase A, hyaluronidase, Dispase and Dnase I. Then suspended cells were passed through 40um strainer and treated with ammonium chloride to remove red blood cells for further processing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Subcutaneous tumor

value: KrasG12D, KEAP1 knockout

value: no


title: LKR13-KLK-1

description: 10x Genomics

value: KrasG12D, KEAP1/LKB1 knockout


title: LKR13-KLK-2

description: 10x Genomics


title: LKR13-K-2

description: 10x Genomics


title: PBMCs, non-infection,  rep1

city: Wuhan

first: Xiaoxu

last: Zhu

address: Jinlong Street

country: China

institute: WUHAN INSTITUTE OF VIROLOGY,  CENTER FOR BIOSAFETY  MEGA SCIENCE, CAS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. For single-cell raw sequencing data, we first employ the CellRanger software for sequencing data quality control, barcode and UMIs splitting, and reference genome alignment. Subsequently, we generate a single-cell gene expression matrix based on cell labels and molecular labels, removing low-quality cell data. Finally, we perform cell data dimensionality reduction, clustering, and analyze differentially expressed genes using GO and KEGG enrichment analysis. Additionally, we annotate cells and analyze cell communication in both human and mouse samples
Assembly: hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
To delineate the single-cell dynamics of PBMCs during latent and reactivated HCMV infection, we procured PBMCs from the peripheral blood of humanized mice. These were categorized into two groups: two wild-type (Mock), and two HCMV-infected (HCMV). Initially, NHDF cells harboring HCMV were introduced into the peritoneal cavity of NOD-scid IL2Rgcnull mice. Following a 4-week period peripheral blood was harvested and partitioned from each mouse group
RNA libraries were prepared for sequencing using standard Illunina protocols

tag: cell type

value: PBMC

value: non infection


title: MAC-T cells, IL10Rα knockout, no infection, rep3 (KO_11)


title: PBMCs, non-infection,  rep2


title: WK-521_Hilum_2dpi_1


title: BANAL-20-236_Hilum_2dpi_4


title: LKR13-K-1

description: 10x Genomics


title: MAC-T cells, IL10Rα knockout, no infection, rep2 (KO_10)


title: n=2/2percent/GGCT-OE


title: LKR13-KK-2

description: 10x Genomics


title: PBMCs, HCMV infected, rep2

value: HCMV infection


title: DNA, F244 cells

city: Saint Louis

first: Robert

middle: D

last: Schreiber

state: MO

address: 425 South Euclid

department: Department of Pathology and Immunology

institute: Washington University in St. Louis

library_source: genomic

data_processing:
For whole exome sequencing, paired-end 151 base pair reads were sequenced on the NovaSeq6000 to aim for 100x coverage in normal and 250x in tumor samples. For RNA-seq, paired-end 151 base pair reads were generated on the NovaSeq6000 to generate for a minimum of 80 million reads per sample; reads were aligned to the mouse genome reference sequence build GRCm38. Alignment was performed using a custom in-house pipeline and the splice-aware aligner STAR (RRID_SCR_004463). The Salmon tool (RRID:SCR_017036) was  used to quantify transcript abundance from the tumor RNA-seq reads generated.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file contains mutation data
Supplementary files format and content: Excel file contains TPM values for F244 and 1956 lines
Library strategy: Whole exome sequencing

molecule: genomic DNA

source_name: In vitro cultured cells

extract_protocol:
DNA and RNA were isolated from in vitro cultured 1956 and F244 cells using QIAamp DNA Kits (Qiagen, Cat# 56304) and RNeasy Kits (Qiagen, Cat# 74104), respectively, according to manufacturer’s instructions. DNA was isolated from tails of female C57BL/6N and male 129S6 mice to serve as control for 1956 and F244, respectively.
Exome sequencing libraries were generated using the NEBNext Ultra II FS Kit (NEB, Cat# E7805). Tumor RNA was subjected to DNase treatment and ribodepletion prior to library construction using NEBNext Ultra II Directional RNA library prep kit for Illumina (NEB, Cat# E7760).

value: In vitro cultured cells


title: BANAL-20-236_Hilum_2dpi_3


title: MAC-T cells, IL10Rα knockout, no infection, rep1 (KO_9)


title: PBMCs, HCMV infected, rep1


title: MAC-T cells, wildtype, MAP infection, rep4 (WT-MAP_8)

value: wildtype

value: MAP infection


title: MAC-T cells, wildtype, MAP infection, rep3 (WT-MAP_7)


title: BANAL-20-236_Hilum_2dpi_1


title: raw_lps10um

city: Wenzhou

first: Kejie

last: Chen

state: Zhejiang

address: Chashan

institute: Wenzhou Medical University

description: with LPS and Harmine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: Lung

value: Macrophages

value: WT

value: pretreated with 10microM Harmine for 0.5 h and then treated with 0.5microg/ml LPS for 6 h


title: Uninfected, biol rep 3

city: Stanford

first: Denise

last: Monack

state: CA

address: 299 Campus Drive, Fairchild Building D331

department: Microbiology and Immunology

institute: Stanford University

data_processing:
nf-core RNA-seq pipeline (Version 3.9)
nf-core FastQC provided summary metrics regarding quality score distribution across reads, per base sequence content, adapter contamination, and overrepresented sequences
TrimGalore! (Version 0.6.5) filtered out adaptors and poor-quality reads
STAR (Version 2.7.10b) mapped reads to the human genome (GRCh37 from the iGenomes reference)
Salmon (Version 1.9.0) quantified transcripts
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes transcripts per million for each Sample
Supplementary files format and content: tab-delimited text file includes raw gene counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: THP-1 cells were seeded in 15cm dishes with 10e7 cells per dish and incubated at 37oC 5% CO2 for 24 hours in RPMI 1640 + glutamine media with an additional 10% FBS 2mM glutamine and 5ng/mL PMA; after 24 hours, PMA media was aspirated and replaced with RPMI 1640 + glutamine media with an additional 10% FBS 2mM glutamine and cells were incubated in this fresh media for 72 hours at 37oC 5% CO2

extract_protocol:
Cells sorted by FACS were dispensed into Qiazol and then bulk-RNA was extracted using chloroform followed by the Qiagen miRNeasy Micro Kit with an on-column DNase treatment
RNA Libraries were prepared for RNA-Seq using Roche Stranded mRNA Stranded RNA-seq following the standard protocol with 100 ng of total RNA input.

treatment_protocol: After 24 hours of PMA treatment followed by 72 hours of incubation in PMA-free media, all samples except for Uninfected 1, Uninfected 2, and Uninfected 3 were infected with S. Typhi at an MOI of 150 for 18 hours; all 18 samples were harvested and sorted by FACS

value: Monocytic

value: Differentiated with PMA, non challenged with S. Typhi (naïve control)


title: MAC-T cells, wildtype, no infection, rep4 (WT_4)

value: mammary epithelium

value: No treatment


title: Uninfected, biol rep 1


title: raw_lps

description: with LPS

value: treated with 0.5microg/ml LPS for 6 h


title: raw_control

description: without any drugs

value: cultured in common medium


title: HAB55

city: Seoul

first: Soo Hyun

last: Kim

address: Ewha Womans University, 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

description: Gene expression data from HAB RNA at ZT07, biological rep2

hyb_protocol: Biotinylated cDNA was hybridized on Affymetrix GeneChip Mouse Gene 2.0 ST Array for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were processed using Affymetrix GeneChip Command Console Software.

label: Biotin

source_name: HAB RNA at ZT07, biological rep2

label_protocol: Total RNA was converted to cDNA and biotylated by GeneChip™ WT Pico Reagent Kit.

extract_protocol: Total RNA was isolated using RNeasy Mini kits, according to the manufacturer’s instructions (Qiagen GmbH, Hilden, Germany). RNA samples from three mice with the same TOD were pooled for subsequent microarray experiments.

value: Habenula (HAB)


title: CpG_2

city: Hangzhou

first: Zhejun

last: Cai

address: 88 Jiefang Road

department: Department of Cardiology, The Second Affiliated Hospital

institute: Zhejiang University School of Medicine

data_processing:
library strategy: Cut & Tag
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.0). In this step, clean data (cleanreads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads fromrawdata. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstreamanalyseswere based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the referencegenome was built using BWA(v0.7.12) and clean reads were aligned to the reference genome using BWAmem. These reads were then filtered for high quality (MAPQ ≥ 13),we also removed reads that were not properlypairedand with PCR duplicates. Only uniquely mapped(MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO--call-summits--nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was usedfor all data sets
The position of peak summit around transcript start sites of genes can predict the interaction sites between proteinandgene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology(GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis wasimplemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-valueless than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resourcefor understanding high-level functions and utilities of the biological system, such as the cell, the organismandtheecosystem, from molecular-level information, especially large-scale molecular datasets generated by genomesequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBASsoftware to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: mm38
Supplementary files format and content: peak annotation of samples
Supplementary files format and content: tdf: Tiled Data File format used specifically in genomic data visualization. TDF files are created to efficiently store and display large genomic datasets, such as those generated by sequencing methods like CUT&Tag, in genome browsers.

source_name: Bone marrow

extract_protocol:
Take out the cryovial and shake it in 37°C water bath to quickly thaw it within 1-2min.Cells were centrifugedfor 5min at 600×g at room temperature. Cell activity was detected with LUNA-FL TM and counted. CUT&Tag assay was performed as described previously (Kaya-Okur, Wu et al. 2019). Briefly, the cells are bound to ConcanavalinA-coated magnetic beads, and the cell membrane is permeabilized by Digitonin. The enzyme pA-Tn5 Transposaseprecisely binds the DNA sequence near the target protein under the antibody guidance and results in factor-targetedtagmentation.
DNA sequence is tagmented, with adapters added at the same time at both ends, which can be enrichedby PCR to form the sequencing-ready libraries. After the PCR reaction, libraries were purified with the AMPurebeads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Bone marrow

value: Bone marrow derived macrophage

value: Macrophage

value: wt

value: stimulated with CpG


title: MAC-T cells, wildtype, no infection, rep3 (WT_3)

value: wildtype


title: HAB43

description: Gene expression data from HAB RNA at ZT19, biological rep2

source_name: HAB RNA at ZT19, biological rep2


title: HAB51

description: Gene expression data from HAB RNA at ZT03, biological rep2

source_name: HAB RNA at ZT03, biological rep2


title: HAB35

description: Gene expression data from HAB RNA at ZT11, biological rep2

source_name: HAB RNA at ZT11, biological rep2


title: HAB47

description: Gene expression data from HAB RNA at ZT23, biological rep2

source_name: HAB RNA at ZT23, biological rep2


title: HAB39

description: Gene expression data from HAB RNA at ZT15, biological rep2

source_name: HAB RNA at ZT15, biological rep2


title: BANAL-20-236_Hilum_2dpi_2

value: lung hilum


title: Non Replicating, biol rep 3

value: Differentiated with PMA, challenged with S. Typhi


title: CpG_1_IgG

description:
CpG.peak_annotation.txt
CpG_IgG_1.tdf


title: MAC-T cells, wildtype, no infection, rep2 (WT_2)

description: no processed data


title: CpG_1


title: MAC-T cells, wildtype, MAP infection, rep2 (WT-MAP_6)

value: MAP infection


title: Non Replicating, biol rep 2


title: MAC-T cells, wildtype, no infection, rep1 (WT_1)


title: HAB31

description: Gene expression data from HAB RNA at ZT07, biological rep1

source_name: HAB RNA at ZT07, biological rep1


title: CpG_2_IgG

description:
CpG.peak_annotation.txt
CpG_IgG_1.tdf


title: Control_2_IgG

description:
Ctrl.peak_annotation.txt
Ctrl_IgG_2.tdf

value: Control PBS


title: MAC-T cells, wildtype, MAP infection, rep1 (WT-MAP_5)


title: Uninfected, biol rep 2

value: Monocytic


title: Non Replicating, biol rep 1


title: Mixed, biol rep 3


title: Control_2


title: HAB23

description: Gene expression data from HAB RNA at ZT23, biological rep1

source_name: HAB RNA at ZT23, biological rep1


title: Control_1_IgG

description:
Ctrl.peak_annotation.txt
Ctrl_IgG_2.tdf


title: HAB27

description: Gene expression data from HAB RNA at ZT03, biological rep1

source_name: HAB RNA at ZT03, biological rep1


title: Mixed, biol rep 1


title: Control_1


title: Host Killed, biol rep 3


title: Host Killed, biol rep 2


title: Mixed, biol rep 2


title: Replicating, biol rep 3


title: Host Killed, biol rep 1


title: HAB19

description: Gene expression data from HAB RNA at ZT19, biological rep1

source_name: HAB RNA at ZT19, biological rep1


title: MC_IL33_PGE2_4

city: Boston

first: Daniel

last: Dwyer

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

data_processing:
Reads were pseudoaligned to the GrCH38 (human) or GRCm39 (mouse) assembly using Kallisto (Bray et al, 2016) with default settings.
Transcript-level (human) or gene-level (mouse) expression data was imported into R using TXImport (Soneson et al, 2015)
Assembly: GrCH38 (human) or GRCm39 (mouse)
Supplementary files format and content: TXImport file containing abundance, counts, and length

source_name: Bone Marrow

growth_protocol: MCs were cultured in RPMI 1640 supplemented with 10% FBS, 1% pen-strep, and 55 micromolar of 2-mercaptoethanol with 50 ng/mL SCF and  30 ng/mL IL-3 (mouse) or  10 ng/mL IL-10, 50 ng/mL IL-6, and 100 ng/mL SCF (human).

extract_protocol:
Cells were spun down and resuspended in TCL buffer (Qiagen) with 1% 2-mercaptoethanol. Lysate containing 1,000 cells was transferred into low-bind plates for sequencing through the Broad Institute Genomics Platform
SmartSeq2 libraries were prepared according to the SmartSeq2 protocol (Picelli et al, 2013, 2014) with some modifications (Trombetta et al, 2014). Briefly, total RNA was purified using RNA-SPRI beads. Poly(A)+ mRNA was converted to cDNA which was then amplified. cDNA was subject to transposon-based fragmentation that used dual-indexing to barcode each fragment of each converted transcript with a combination of barcodes specific to each sample. Barcoded cDNA fragments were then pooled prior to sequencing. Sequencing was carried out using an Illumina NextSeq500 as paired- end 2x25bp with an additional 8 cycles for each index.

treatment_protocol: Murine BMMCs (50,000 cells/well) were stimulated with 10 ng/mL of IL-33 and/or 1 µM of PGE2 for 24 hours in biologic quadruplicate. CBMCs were rested at 50,000 cells/100 uL in media containing SCF (100 ng/mL) overnight prior to stimulation with 1 µM PGE2 for 72 hours in technical duplicate

value: Bone Marrow

value: Mast cell

tag: strain

value: 10 mg/mL IL-33 and 1uM of PGE2

tag: time point

value: 24 hours


title: MC_IL33_PGE2_2


title: UKN1_SBAD2_ValproicAcid_0.6_3

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the statistical software R, version 4.2.1 Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

label: biotin

source_name: SBAD2 iPS cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: The differentiation of SBAD2 hiPSCs to neuroepithelial precursor cells was performed using the UKN1 protocol (Chambers et al. 2009) with minor changes. Briefly, hiPSCs were seeded in 1 ml pluripotent stem cell (PSC) medium (spiked with a Rho-kinase inhibitor (ROCKi)) per well on extracellular matrix protein-coated 12-well-plates at a density of 12,000 - 24,000 cells/cm² on day -3. On day  2 and day  1, the PSC medium was refreshed. On days 0, 1 and 2, medium was changed to differentiation medium, which was spiked with 21.6 µM SB431542, 0.64 µM dorsomorphin, 35 ng/ml noggin and 0.1% DMSO to induce neural differentiation. On day 4, medium was changed to a mixed medium of 75% differentiation medium / 25% N2-S and the same concentrations of SB431542, dorsomorphin and noggin as given above. On day 6, cells were collected for RNA extraction. A more detailed method description is given in the supplemental information.

extract_protocol: Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).

treatment_protocol: On days 0, 1 and 2, differentiating cells were incubated (5% CO2, 37 °C) with paraben concentrations ranging from 0.316 – 1000 µM and valproic acid at 600 µM for a total of 96 h, as well as the vehicle alone (0.1% DMSO).

value: SBAD2 iPS cells

tag: Sex

value: male


title: HAB15

description: Gene expression data from HAB RNA at ZT15, biological rep1

source_name: HAB RNA at ZT15, biological rep1

value: Habenula (HAB)


title: UKN1_SBAD2_ValproicAcid_0.6_2


title: MC_IL33_PGE2_3


title: STR55

description: Gene expression data from STR RNA at ZT07, biological rep2

source_name: STR RNA at ZT07, biological rep2

value: Striatum (STR)


title: MC_IL33_PGE2_1


title: STR51

description: Gene expression data from STR RNA at ZT03, biological rep2

source_name: STR RNA at ZT03, biological rep2


title: Bystander, biol rep 3


title: Replicating, biol rep 2


title: HAB11

description: Gene expression data from HAB RNA at ZT11, biological rep1

source_name: HAB RNA at ZT11, biological rep1


title: STR43

description: Gene expression data from STR RNA at ZT19, biological rep2

source_name: STR RNA at ZT19, biological rep2


title: Replicating, biol rep 1


title: JAK2V617F mutant cardiac EC following high-fat diet treatment

city: STONY BROOK

first: Huichun

last: Zhan

state: NY

address: 15-089 HSC, 101 Nicolls Rd

institute: Stony Brook Medicine

description: Mutant EC

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis between two groups was performed using the edgeR R package (3.22.5). The resulting P-values were adjusted using the Benjamini and Hochberg’s method for controlling the false discovery rate. Genes with an adjusted P-value < 0.05 found by edgeR were assigned as differentially expressed.
Gene set enrichment analysis (GSEA) was performed using the complete list of genes according to their differential expression. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the ClusterProfiler R package. GO terms with corrected P-value less than 0.05 were considered significantly enriched.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include gene ID, readcount, FPKM, log2 fold change, p value, padj value, and gene information for each sample

source_name: Heart

extract_protocol:
Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads and used to generate sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England BioLabs, MA, USA).The library preparations were sequenced on an Illumina platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome.

value: Heart

value: Heart endothelial cells

value: High fat diet


title: JAK2 Wildtype Cardiac EC following high-fat diet treatment

description: Control EC


title: Bystander, biol rep 1


title: UKN1_SBAD2_Untreated_0_4


title: STR47

description: Gene expression data from STR RNA at ZT23, biological rep2

source_name: STR RNA at ZT23, biological rep2


title: UKN1_SBAD2_Untreated_0_2


title: Bystander, biol rep 2


title: MC_PGE2_3

value: 1uM PGE2


title: STR39

description: Gene expression data from STR RNA at ZT15, biological rep2

source_name: STR RNA at ZT15, biological rep2


title: UKN1_SBAD2_Untreated_0_1


title: UKN1_SBAD2_Untreated_0_3


title: DU145 cells,transfected with the control plasmids, Rep2

city: Suzhou

first: Chaogang

last: Wei

address: 1055 Sanxiang Road, Suzhou 215004, Jiangsu, China

institute: The Second Affiliated Hospital of Soochow University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Homo_sapiens.GRCh38.101
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: prostate carcinoma

growth_protocol:
PC3 cells were maintained in Ham’s F-12K medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.
DU145 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

treatment_protocol:
PC3 cells seeded in 6-well plates were infected with the CRISPR/Cas9 lentiviral vectors (EphA2-Cas9-sgRNA) and the control lentivirus carrying non-targeting sgRNA sequence. These cells were then incubated at 37℃ for 72 h.The efficiency of EphA2 gene knockout was verified by Sanger sequencing,then the EphA2 gene knockout efficiency was quantified using the Tracking of Indels by Decomposition (TIDE) online software (http://shinyapps.datacurators.nl/tide/).
DU145 cells were seeded in a 6-well plate. When the cells reached 80%-90% confluence, the EphA2 expression plasmid and control plasmid, respectively, were transfected into the cells using Lipofectamine TM 3000 transfection reagent (Invitrogen, USA) according to the manufacturer’s instructions. After incubation at 37℃ for 48 h, the efficiency of EphA2 overexpression was verified by quantitative real-time PCR (qPCR) and Western blotting.

value: prostate carcinoma

value: Cancer cell line

value: WT

value: transfected with the control plasmids


title: UKN1_SBAD2_ValproicAcid_0.6_1


title: UKN1_SBAD2_Propylparaben_100_4


title: MC_PGE2_2


title: STR31

description: Gene expression data from STR RNA at ZT07, biological rep1

source_name: STR RNA at ZT07, biological rep1


title: DU145 cells,transfected with the control plasmids, Rep1


title: UKN1_SBAD2_Propylparaben_31.6_2


title: STR35

description: Gene expression data from STR RNA at ZT11, biological rep2

source_name: STR RNA at ZT11, biological rep2


title: STR27

description: Gene expression data from STR RNA at ZT03, biological rep1

source_name: STR RNA at ZT03, biological rep1


title: UKN1_SBAD2_Propylparaben_100_3


title: UKN1_SBAD2_Propylparaben_100_1


title: STR23

description: Gene expression data from STR RNA at ZT23, biological rep1

source_name: STR RNA at ZT23, biological rep1


title: MC_IL33_4

value: 10 mg/mL IL-33


title: MC_PGE2_4

value: Bone Marrow


title: DU145 cells,EphA2 gene overexpressed(transfected with the EphA2 expression plasmids), Rep1


title: DU145 cells,EphA2 gene overexpressed(transfected with the EphA2 expression plasmids), Rep2


title: MC_IL33_3

value: Mast cell


title: MC_IL33_2


title: STR15

description: Gene expression data from STR RNA at ZT15, biological rep1

source_name: STR RNA at ZT15, biological rep1


title: UKN1_SBAD2_Propylparaben_31.6_3


title: PC3 cells,infected with the CRISPR/Cas9 control lentiviral vectors, Rep1


title: STR19

description: Gene expression data from STR RNA at ZT19, biological rep1

source_name: STR RNA at ZT19, biological rep1


title: MC_PGE2_1

source_name: Bone Marrow


title: UKN1_SBAD2_Propylparaben_31.6_1

source_name: SBAD2 iPS cells


title: PC3 cells,infected with the CRISPR/Cas9 control lentiviral vectors, Rep2


title: MC_IL33_1


title: PC3 cells,EphA2 gene knock out(infected with the CRISPR/Cas9 lentiviral vectors), Rep1

value: EphA2 knockout


title: MC_PBS_4

value: PBS


title: MC_PBS_2


title: PC3 cells,EphA2 gene knock out(infected with the CRISPR/Cas9 lentiviral vectors), Rep2


title: MC_PBS_3


title: Human Prostate Biopsy, HMP24

city: Ithaca

first: Jooyoung

last: Park

address: 237 Tower Rd

institute: Cornell University

description: 10x Genomics

data_processing:
SEQC alignment
Cell filtering with Seurat (percent.mt < 25, nCount > 200)
DoubletDetection for doublet detection
log normalization
Cell cycle score regression with Seurat
Data scaling with Seurat
Seurat for downstream analysis
Assembly: hg38
Supplementary files format and content: count matrix (.mtx.gz)
Supplementary files format and content: feature and barcode (.tsv.gz)
Supplementary files format and content: seurat object for whole cells and tumor cells (.rds)

source_name: Prostate tumor, pelvic mass

extract_protocol:
Fresh benign and malignant tissue was mechanically cut using a scalpel into small pieces (~1–5 mm3). The tissue was then processed and dissociated in 5–10 mg/ml collagenase type II (Gibco) solution in adDMEM/F12+/+/+ with 10 µM Y–27632 dihydrochloride for 30 minutes to 2 hours on a 37oC shaking platform. This was followed by a 1 minute 0.5 M EDTA wash at room temperature, and subsequent digestion with TrypLE (Gibco) with 10 µM Y–27632 dihydrochloride for 5–10 minutes at 37oC on a shaking platform until a single cell suspension was obtained.  If more than 10% of doublets were present (visual inspection) or there was evidence for <80% viability (hemocytometer, using 0.2% Trypan Blue), then cells were FACS–sorted for singlets and viability using a DAPI. Please refer to methods of paper for further details.
Dissociated cells were subjected to scRNA–seq using 10X genomics Chromium Single Cell 3’ Library and Gel bead Kit (v3 for all human biospies, except v2 for HP95T as previously described PMID: 32355025) per manufacturer’s protocol. ~3000 to 10,000 cells per sample was encapsulated and barcoded following the manual.  Sample viability varied between 72 and 95% (0.2% Trypan Blue).  The final sequencing libraries were double–size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova–Seq platform (R1–26 cycles, i7–8 cycles, R2–70 cycles or higher).

value: Prostate tumor, pelvic mass


title: STR11

description: Gene expression data from STR RNA at ZT11, biological rep1

source_name: STR RNA at ZT11, biological rep1


title: Human Prostate Biopsy, HMP23B

description: 10x Genomics

source_name: Prostate tumor, primary

value: Prostate tumor, primary


title: PFC47

description: Gene expression data from PFC RNA at ZT23, biological rep2

source_name: PFC RNA at ZT23, biological rep2

value: Prefrontal cortex (PFC)


title: UKN1_SBAD2_Propylparaben_10_4

value: SBAD2 iPS cells

value: male


title: MC_PBS_1


title: UKN1_SBAD2_Propylparaben_3.16_4


title: UKN1_SBAD2_Propylparaben_10_3


title: Cerebral cortex, 21days after ZIKV infection, Bio rep3

first: Nahyun

address: 120 Neungdong-ro, Gwangjin-gu, Seoul

institute: Konkuk university

data_processing:
Illumina NovaSeq 6000
Sequenced RNA-sequencing reads were trimmed for adapter seuquence, and processed for eliminating artifacts such as contaminant DNA or PCR duplicates using Trimmomatic 0.38 with parameters SLIDINGWINDOW:4:15 TRAILING:3 LEADING:3 MINLEN:36.
Trimmed reads were mapped to reference genome (UCSC GRCm38/mm10) using the Bowtie2 2.3.4.1 aligner.
Fragments per kilobase of transcript per million mapped reads (FPKM) was estimated with StringTie for mus musculus genes.
Assembly: mm10
Supplementary files format and content: GTF file contains the merged transcript annotations generated using StringTie

source_name: Cerebral cortex

extract_protocol:
RNA was harvested using the PureLink™ RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

treatment_protocol: The experimental group was intraperitoneally injected with either ZIKV-FLR strain at a concentration of 5 × 10^4 PFU/ml, while the uninfected control group was intraperitoneally injected with an equivalent volume of PBS. Mice were monitored daily for signs of illness, including changes in body weight and mortality

value: Cerebral cortex

value: Female

value: IFN-a/b receptor knockout

value: ZIKV-FLR infection

value: 21days post-infection


title: UKN1_SBAD2_Propylparaben_10_1


title: Human Prostate Biopsy, HMP22

description: 10x Genomics

source_name: Prostate tumor, lymph node

value: Prostate tumor, lymph node


title: PFC55

description: Gene expression data from PFC RNA at ZT07, biological rep2

source_name: PFC RNA at ZT07, biological rep2


title: PFC39

description: Gene expression data from PFC RNA at ZT15, biological rep2

source_name: PFC RNA at ZT15, biological rep2


title: Cerebral cortex, 21days after ZIKV infection, Bio rep2


title: Human Prostate Biopsy, HMP23A

description: 10x Genomics


title: PFC43

description: Gene expression data from PFC RNA at ZT19, biological rep2

source_name: PFC RNA at ZT19, biological rep2


title: PFC35

description: Gene expression data from PFC RNA at ZT11, biological rep2

source_name: PFC RNA at ZT11, biological rep2


title: PFC51

description: Gene expression data from PFC RNA at ZT03, biological rep2

source_name: PFC RNA at ZT03, biological rep2


title: PFC27

description: Gene expression data from PFC RNA at ZT03, biological rep1

source_name: PFC RNA at ZT03, biological rep1


title: PFC31

description: Gene expression data from PFC RNA at ZT07, biological rep1

source_name: PFC RNA at ZT07, biological rep1


title: Cerebral cortex, 21days after ZIKV infection, Bio rep1


title: UKN1_SBAD2_Propylparaben_3.16_3


title: PFC23

description: Gene expression data from PFC RNA at ZT23, biological rep1

source_name: PFC RNA at ZT23, biological rep1


title: UKN1_SBAD2_Propylparaben_10_2


title: Cerebral cortex, 7days after ZIKV infection, Bio rep3

value: 7days post-infection


title: JURKAT, oxamate and lactate

city: Shanghai

first: Wu

last: Wenyan

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children's Medical Center

data_processing:
For quality control of the raw sequencing data, FastQ Screen (version 0.13.0) and FastQC (version 0.11.9) were utilized.
The STAR software (version 2.7.1a) was employed for mapping the reads to the human genome (hg19) or hybrid human(hg19)-ERCC genome. Read counts within each gene were computed using HTSeq count (version 0.11.2).
The data from the sodium oxamate inhibition experiment underwent normalization through the RUVseq R package (version 1.34.0), utilizing the ERCC synthetic RNA controls for the Removal of Unwanted Variance (RUV) method.
Assembly: hg19
Supplementary files format and content: normalized_counts.txt

source_name: JURKAT

growth_protocol: RPMI 1640 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent. For the sodium oxamate inhibition experiment, after extracting total RNA from an equal number of cells, a diluted ERCC RNA spike-in mix (Invitrogen 4456740) was additionally incorporated as a control.
For mRNA-seq libraries, poly-A mRNA was isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490). Libraries for sequencing were generated in accordance with the manufacturer's recommendations using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, #E7530).

treatment_protocol: For the sodium oxamate inhibition experiment, Jurkat cells were cultured for 48 hours in standard medium, medium containing 50mM sodium oxamate, and medium supplemented with both 50mM sodium oxamate and 10mM L-sodium lactate.

value: JURKAT

value: oxamate+lactate


title: UKN1_SBAD2_Propylparaben_1_4


title: UKN1_SBAD2_Propylparaben_1_1


title: UKN1_SBAD2_Propylparaben_0.316_4


title: UKN1_SBAD2_Propylparaben_3.16_1


title: JURKAT, oxamate

value: oxamate


title: Cerebral cortex, 7days after ZIKV infection, Bio rep2


title: JURKAT, control

value: standard medium


title: Cerebral cortex, 7days after ZIKV infection, Bio rep1


title: HeLa shYAP B 2 [A_10]

city: Leeds

first: Andrew

last: Macdonald

state: West Yorkshire

address: Faculty of Biological Sciences

department: School of Molecular and Cellular Biology

country: United Kingdom

institute: University of Leeds

data_processing:
Quality filtered and trimmed with Trimmomatic (Q < 20)
Trimmed reads aligned to hg38 using HISAT2
Expression counts across genomic features quantified using HTSeq onh GRCh38/hg38 (-s no, -a 10, -m union, -nonunique none)
Assembly: hg38
Supplementary files format and content: comma separated text file containing raw counts of each sample

source_name: HeLa

growth_protocol: Monoclonal shRNA KD HeLa cells were maintained in DMEM with 10% FBS and penicillin/ streptomycin

extract_protocol: Full rRNA depletion, PE150

treatment_protocol: HeLa cells were transduced with lentival shRNA vectors and selected with 2 µg/mL puromycin

value: HeLa

value: shYAP B


title: PFC19

description: Gene expression data from PFC RNA at ZT19, biological rep1

source_name: PFC RNA at ZT19, biological rep1


title: HeLa shYAP B 1 [A_09]


title: UKN1_SBAD2_Methylparaben_1000_3

source_name: SBAD2 iPS cells


title: Cerebral cortex, Uninfected control, Bio rep2

value: Uninfected control


title: HeLa shYAP A 2 [A_08]

value: shYAP A


title: Cerebral cortex, Uninfected control, Bio rep1


title: UKN1_SBAD2_Propylparaben_0.316_3

value: SBAD2 iPS cells


title: PFC15

description: Gene expression data from PFC RNA at ZT15, biological rep1

source_name: PFC RNA at ZT15, biological rep1

value: Prefrontal cortex (PFC)


title: HeLa shYAP A 1 [A_07]


title: 24-25M F#5

first: Cintia

middle: S.

last: de Paiva

state: TX

address: 6565 Fannin Street NC505G

department: Ophthalmology

institute: Baylor College of Medicine

description: naïve mice

data_processing:
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, California). Reads were trimmed using cutadapt and quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build GRCm38 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using the DESeq2 R library. Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC.  DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. The clustering of genes for the final heatmap of differentially expressed genes was done using the partitioning around medoids method using the fpc R library. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, was used to determine local similarities and dependencies between GO terms to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro3, NCBI, MSigDB REACTOME, and WikiPathways.
ROSALIND
.A single-read 75 base pair cycle run was used to sequence the flow cell. An average of 21 million reads per sample was sequenced. The FastQ file generation was executed using Illumina’s cloud-based informatics platform, BaseSpace Sequencing Hub (Illumina).
Assembly: mm10
Supplementary files format and content: txt-delimited files with rawCounts
Supplementary files format and content: processed counts as excel files

source_name: Cornea

extract_protocol:
Qiagen Plus mini kit
A double-stranded DNA library was created at Baylor College of Medicine’s Genomics and RNA Profiling Core. Briefly, using 100ng of total RNA (measured by pico green), an oligodT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA, and reverse transcription was performed using a Lexogen kit.
Second-strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The purified double-stranded library was then amplified and purified. The resulting libraries were quantitated using Qubit 2.0 (ThermoFisher) and fragment size was assessed with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California).

value: Cornea

value: epithelial

value: wild-type

tag: age

value: 24-25 months

tag: lab identifier


title: SNVTA55

description: Gene expression data from SN/VTA RNA at ZT07, biological rep2

source_name: SN/VTA RNA at ZT07, biological rep2

value: Substantia nigra and ventral tegmental area (SN/VTA)


title: UKN1_SBAD2_Methylparaben_1000_2

value: male


title: UKN1_SBAD2_Propylparaben_1_3


title: UKN1_SBAD2_Methylparaben_1000_1


title: Cerebral cortex, Uninfected control, Bio rep3

source_name: Cerebral cortex

value: Cerebral cortex

value: Female

value: IFN-a/b receptor knockout


title: UKN1_SBAD2_Methylparaben_316_3


title: 24-25M F#4

description: naïve mice


title: 24-25M F#3

description: naïve mice


title: SNVTA51

description: Gene expression data from SN/VTA RNA at ZT03, biological rep2

source_name: SN/VTA RNA at ZT03, biological rep2


title: PFC11

description: Gene expression data from PFC RNA at ZT11, biological rep1

source_name: PFC RNA at ZT11, biological rep1


title: HeLa shTAZ B 1 [A_05]

value: shTAZ B


title: SNVTA47

description: Gene expression data from SN/VTA RNA at ZT23, biological rep2

source_name: SN/VTA RNA at ZT23, biological rep2


title: HeLa shTAZ A 2 [A_04]

value: shTAZ A


title: UKN1_SBAD2_Methylparaben_316_1


title: HeLa shTAZ B 2 [A_06]

value: HeLa


title: 24-25M F#2

description: naïve mice


title: HeLa shTAZ A 1 [A_03]


title: SNVTA39

description: Gene expression data from SN/VTA RNA at ZT15, biological rep2

source_name: SN/VTA RNA at ZT15, biological rep2


title: UKN1_SBAD2_Methylparaben_316_2


title: UKN1_SBAD2_Methylparaben_100_3


title: SNVTA35

description: Gene expression data from SN/VTA RNA at ZT11, biological rep2

source_name: SN/VTA RNA at ZT11, biological rep2


title: SNVTA43

description: Gene expression data from SN/VTA RNA at ZT19, biological rep2

source_name: SN/VTA RNA at ZT19, biological rep2


title: UKN1_SBAD2_Methylparaben_100_2


title: HeLa shNEG 2 [A_02]

value: shNEG


title: 24-25M F#1

description: naïve mice


title: UKN1_SBAD2_Methylparaben_100_4


title: UKN1_SBAD2_Methylparaben_100_1


title: 18-19M F#5

description: naïve mice

value: 18-19 months


title: SNVTA31

description: Gene expression data from SN/VTA RNA at ZT07, biological rep1

source_name: SN/VTA RNA at ZT07, biological rep1


title: 18-19M F#3

description: naïve mice


title: SNVTA27

description: Gene expression data from SN/VTA RNA at ZT03, biological rep1

source_name: SN/VTA RNA at ZT03, biological rep1


title: 18-19M F#2

description: naïve mice


title: Human aortic endothelial cells, 48h flow aligned, GSK205, rep3

city: Los Angeles

first: Soon-Gook

last: Hong

state: California

address: 630 Charles E Young Dr S

department: Medicine

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV.
Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The alignment was performed using Spliced Transcripts Alignment to a Reference (STAR) using the human reference genome assembly GRCh38.
The Ensembl Transcripts release GRCh38.107 GTF was used for gene feature annotation.
For normalization of transcripts counts, counts per million (CPM) normalized counts were generated by adding 1.0E-4 followed by CPM normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: HAECs

growth_protocol: Primary HAECs (Cell Applications #S304-05a) were maintained in MCDB-131 complete media (VEC Technologies #MCDB-131 Complete) supplemented with 10% FBS (Omega USDA certified FBS #FB-11). For plating cells on 6-well plate cell culture dishes, 0.1% gelatin (Stemcell #07903) coating was first applied. Cells were cultured in a 37 °C incubator with 5% CO2.

extract_protocol:
Prior to cell lysis, non-aligned cells from the center of each well were removed using 1.8 cm blade cell scraper (Falcon #353085) and washed with 1X DPBS (Gibco #14190-144). The remaining flow-aligned cell monolayer was lysed using RLT lysis buffer (QIAGEN #79216) plus 1% 2-Mercaptoethanol (Sigma Aldrich #M6250). For each condition, 2 wells were combined as one flow-aligned sample for a total of 6 wells for n = 3 samples.
Libraries for RNA sequencing were prepared using KAPA Stranded mRNA-Seq Kit (KAPA Biosystems #KK8421).

treatment_protocol: After 48 h unidirectional flow application on orbital shaker (130 rpm), the flow-conditioned HAEC monolayers were treated with either DMSO (volume equivalent) or GSK205 (20 µM; MedChemExpress #HY-120691A) for 2 h under flow.

value: HAECs

value: Human aortic endothelial cells

value: WT


title: Human aortic endothelial cells, 48h flow aligned, GSK205, rep1


title: HeLa shNEG 1 [A_01]


title: Human aortic endothelial cells, 48h flow aligned, GSK205, rep2


title: 18-19M F#1

description: naïve mice

value: Cornea


title: UKN1_SBAD2_Methylparaben_31.6_3

value: SBAD2 iPS cells


title: KD-Ctrl_L4_106106

first: Xinxiang

last: Li

address: #270 Dongan Road, Xuhui District

institute: Fudan University Shanghai Cancer Center

description: RKO cells, shSQLE-3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2.
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Assembly: mm8
Supplementary files format and content: FPKM

source_name: RKO

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum (HyClone, Logan, UT, USA)

extract_protocol:
TRIzol (Invitrogen, Thermo Fisher Scientific) was used to extract the total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: RKO

value: colorectal cancer cells

value: SQLE knockdown


title: 18-19M F#4

description: naïve mice

value: epithelial

value: wild-type


title: Human aortic endothelial cells, 48h flow aligned, DMSO, rep3

value: DMSO


title: SNVTA15

description: Gene expression data from SN/VTA RNA at ZT15, biological rep1

source_name: SN/VTA RNA at ZT15, biological rep1

value: Substantia nigra and ventral tegmental area (SN/VTA)


title: 12-13M F#5

description: naïve mice

value: 12-13 months


title: SNVTA23

description: Gene expression data from SN/VTA RNA at ZT23, biological rep1

source_name: SN/VTA RNA at ZT23, biological rep1


title: SNVTA19

description: Gene expression data from SN/VTA RNA at ZT19, biological rep1

source_name: SN/VTA RNA at ZT19, biological rep1


title: Human aortic endothelial cells, 48h flow aligned, DMSO, rep2


title: KD-Ctrl_L4_104104

description: RKO cells, shSQLE-1


title: UKN1_SBAD2_Methylparaben_31.6_1

source_name: SBAD2 iPS cells

value: male


title: 12-13M F#4

description: naïve mice

source_name: Cornea


title: KD-Ctrl_L4_105105

description: RKO cells, shSQLE-2


title: SNVTA11

description: Gene expression data from SN/VTA RNA at ZT11, biological rep1

source_name: SN/VTA RNA at ZT11, biological rep1


title: UKN1_SBAD2_Methylparaben_10_4


title: Human aortic endothelial cells, 48h flow aligned, DMSO, rep1


title: UKN1_SBAD2_Methylparaben_31.6_2


title: UKN1_SBAD2_Methylparaben_10_3


title: 12-13M F#3

description: naïve mice


title: UKN1_SBAD2_Methylparaben_10_2


title: NT-Ctrl_L4_103103

description: RKO cells, shControl-3


title: KSHV-Enriched 48 h Induced BCBL-1 BR2

city: Gainesville

first: Rolf

last: Renne

state: FL

address: 1200 Newell Dr.

institute: University of Florida

description:
All_induced_NC009333Aligned.sorted.bam.forward.bdg.gz
All_induced_NC009333Aligned.sorted.bam.reverse.bdg.gz

data_processing:
Paired-end reads were quality checked using FastQC.
Adaptors were trimmed using the Trimmomatic program with the settings, ILLUMINACLIP: adapters.fa:2:30:10, LEADING:3, TRAILING:3 and MINLEN:36.
Merged the fastq files with trimmed and paired reads from all samples.
Aligned of the merged fastq file to KSHV genome (NCBI accession number NC_009333.1) using STAR version 2.7.0b with default parameters
Generation of bedgraph coverage files using bamCoverage tool by deepTools suite
Assembly: Genome_build: NC_009333.1
Supplementary files format and content: Supplementary_files_format_and_content: Signal coverage files for the KSHV genome in bedgraph format

growth_protocol: Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 1% Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated from cultured cells using the TRIzol reagent (Ambion) as per manufacturer's protocol. Ribosomal RNA was depleted from total RNA using the NEB rRNA depletion kit (E6310)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760) was used to prepare stranded RNA-Seq libraries.

treatment_protocol: Induction with 12-O-tetradecanoylphorbol-13-acetate (TPA) (20 ng/ml) and sodium butyrate (2 mM) for 48 h

value: Primary effusion lymphoma cells

value: Induced


title: UKN1_SBAD2_Methylparaben_10_1


title: 12-13M F#2

description: naïve mice


title: NT-Ctrl_L4_101101

description: RKO cells, shControl-1


title: KSHV-Enriched 48 h Induced BCBL-1 BR1


title: 12-13M F#1

description: naïve mice


title: 2-3M F#5

description: naïve mice

value: 2-3 months


title: UKN1_SBAD2_Methylparaben_3.16_3


title: 2-3M F#4

description: naïve mice


title: 48 h Induced BCBL-1 BR2


title: 48 h Induced BCBL-1 BR1


title: 2-3M F#3

description: naïve mice


title: L2 48h NT

city: San Francisco

first: Bushra

last: Samad

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

description: 10x Genomics

data_processing:
Sequencer-generated bcl data (Gene expression and Lipid Hashtag) was demultiplexed into individual fastq libraries using the mkfastq command on the Cellranger 3.0.2 suite of tools (https://support.10xgenomics.com)
Raw gene-expression fastqs were aligned to the GRCh38 reference genome annotated with Ensembl v85, and Lipid Hashtag fastqs were processed to count the incidences of each expected index per cell.
Feature-barcode matrices were read into Seurat 4.0.1 and poorly captured genes (in < 3 cells) were dropped from the analyses.
Matrices were further filtered to remove events with greater than 20% mitochondrial content, events with greater than 50% ribosomal content, or events with fewer than 100 total genes.
Data quality control and nornalization
Assembly: GRCh38 reference genome
Supplementary files format and content: HDF5 feature barcode matrix format

source_name: Lung

growth_protocol: Culture in DMEM 1%PS, 10% FCS

extract_protocol:
PCLSs were enzymatically and mechanically dissociated. Single cell suspension was used for the 10X encapsulation. Cells were counted and the targeted cell number for loading was 8000 cells per sample.
10X encapsulation and library construction were done using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 per the manufacturer’s instruction. Multi-seq library preparation was done as previously described.  Libraries were mixed at an approximate 10:1 molar ratio of gene expression to LMO barcodes for sequencing.  The sequencing was done on the Illumina NovaSeq 6000 using 10X Genomics recommended sequencing parameters.

treatment_protocol: Precision-Cut Lung slices (PCLS) were infected with 500K or 50K pfu for 24.48 or 72h (n=3 slices per condition)

value: Lung

value: NT


title: UKN1_SBAD2_Methylparaben_3.16_2


title: HEK293, IFNα.20h, rep2

city: Glasgow

first: Honglin

address: Centre for Virus Research

institute: Centre for Virus Research

data_processing:
RNA-Seq reads quality was assessed using FastQC software (89.1% of the reads generated presented a Q score of ≥30).
RNA-Seq reads were aligned to the Homo sapiens genome (GRCh38) downloaded via ENSEMBL using Hisat2.
After the alignment, software FeatureCount was used to count reads mapping to genes annotation files.
Package edgeR was used to calculate the gene expression level and to analyze differentially expressed genes between sample groups .
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: comma-delimited text file includes CPM for each sample, and average CPM and differential expression analysis results for the corresponding sample group

growth_protocol: Cells were cultured in DMEM with 10 % FBS and 1x penicillin/streptomycin at 37oC with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using Monarch Total RNA Miniprep Kit (NEB, T2010S) following the manufacturer’s protocol, eluted in 100 μl nuclease-free water. Ribosomal RNAs were removed by rRNA Depletion Kit (NEB, E6310) following the manufacturer’s protocol.
Extracted RNAs were supplied with RiboLock RNase inhibitor (Thermo Scientific, EO0381) and subjected to SuperScript III reverse transcriptase (Invitrogen, #18080093) for cDNA library generation using random hexamer primers. RNase H was added to reverse transcription products to obtain cDNA library for RNA-seq.

treatment_protocol: IFN-α stocks were supplied into culture media at indicated concentration and time period prior to harvest. IFN-α stocks were obtained by dissolving commercial IFN-α (PBL assay science, #11100-1) with 0.1% BSA in water and stored at -80oC.

value: immortalised embryonic kidney cell

value: WT

value: IFN-alpha, 20 h


title: L2 24h NT

description: 10x Genomics


title: HEK293, IFNα.20h, rep1


title: HEK293, IFNα.4h, rep3

value: IFN-alpha, 4 h


title: NT-Ctrl_L4_102102

description: RKO cells, shControl-2

value: RKO

value: colorectal cancer cells


title: 2-3M F#1

city: Houston

description: naïve mice

value: Cornea

value: epithelial


title: HEK293, IFNα.4h, rep2


title: 2-3M F#2

description: naïve mice

value: wild-type


title: L2 48h SARS

description: 10x Genomics

value: SARS


title: L2 24h SARS

description: 10x Genomics


title: UKN1_SBAD2_Methylparaben_3.16_4

value: SBAD2 iPS cells


title: UKN1_SBAD2_Methylparaben_3.16_1

value: male


title: UKN1_SBAD2_Methylparaben_1_2


title: UKN1_SBAD2_Methylparaben_1_4


title: HEK293, IFNα.4h, rep1


title: HEK293, mock, rep3


title: HEK293, IFNα.20h, rep3


title: UKN1_SBAD2_Methylparaben_1_3


title: UKN1_SBAD2_Methylparaben_1_1


title: L1 48h NT

description: 10x Genomics


title: UKN1_SBAD2_Methylparaben_0.316_3


title: 5Bone Marrow-Control

city: Moscow

first: Liya

last: Kondratyeva

address: Ulitsa Miklukho Maklaya, 16/10

country: Russia

institute: Institute of bioorganic chemistry of the Russian Academy of Sciences

data_processing:
The raw reads were mapped on the murine reference genome (mm10) using HISAT2 (Galaxy Version 2.2.1+galaxy1)
The featureCounts tool (Galaxy Version 2.0.3+galaxy2) was used for counting reads to GENCODE release M23 annotated genes.
Assembly: mm10
Supplementary files format and content: .txt format, matrix table with featureCounts read counts

source_name: Bone Marrow

growth_protocol: Mice were subcutaneously vaccinated with 10^6 CFU of Mycobacterium bovis/BCG in 100 µl phosphate-buffered saline, mice in the control group were subcutaneously injected with 100 µl of PBS. Three days after BCG administration, vaccinated and control animals were sacrificed under isoflurane anesthesia, by exsanguination and subsequent cervical dislocation, after which spleen and bone marrow were collected. Single-cell suspensions from the organs were stained with conjugated anti-CD45, anti-CD11b, anti-NK1.1, anti-Ly6G, and anti-Ly6C antibodies, and subjected the suspensions to fluorescence-activated cell sorting (FACS). The prepared cell suspensions were used for FACS sorting and three cell populations were collected: monocytes [CD45+CD11b+Ly6C+], neutrophils [CD45+CD11b+Ly6G+] and NK-cells [CD45+CD11b-NK1.1+]. Moreover, 1 million of total unsorted bone marrow cells from each mouse were collected. The samples were collected for each mouse from both control and BCG vaccinated groups.

extract_protocol:
Harvested cells were lysed using ExtractRNA (Evrogen, Moscow, Russian Federation). RNA was extracted with RNA Clean & Concentrator TM-5 (Zymo Research, Irvine, CA, USA). To get rid of the excess ribosomal RNA, NEBNext rRNA Depletion Kit v2 was used.
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with Sample Puri-fication Beads (New England BioLabs) and a NEBNext Multiplex Oligos for Illumina (Unique Dual Index UMI Adaptors RNA Set 1, New England BioLabs) were used for the preparation of libraries.

value: Bone Marrow

value: Bone Marrow cells

value: Bone Marrow cells (unsorted)

value: wt

value: PBS


title: L1 48h SARS

description: 10x Genomics

value: Lung


title: L1 24h NT

description: 10x Genomics

value: NT


title: HEK293, mock, rep1

last: Chen

value: immortalised embryonic kidney cell

value: WT


title: 2Bone Marrow-BCG

value: BCG


title: HEK293, mock, rep2


title: 6Bone Marrow-BCG


title: 3Bone Marrow-Control


title: 4Bone Marrow-BCG


title: CBMC_PGE2_1

source_name: Cord Blood

value: Cord Blood

value: Mast cell

value: 1uM PGE2

value: 72 hours


title: L1 24h SARS

description: 10x Genomics

value: SARS


title: CBMC_PGE2_2


title: 1Bone Marrow-Control


title: L3 72h Flu LMO

description: 10x Genomics

value: Flu/NT


title: UKN1_SBAD2_Methylparaben_0.316_2

value: SBAD2 iPS cells

value: male


title: UKN1_SBAD2_Ethylparaben_316_3


title: UKN1_SBAD2_Ethylparaben_316_4


title: 6Monocytes-BCG

value: Bone Marrow

value: immune cells

value: Monocytes (CD45+CD11b+Ly6C+)


title: CBMC_PBS_1

value: PBS


title: L3 48h Flu LMO

description: 10x Genomics

value: Lung


title: L3 72h Flu

description: 10x Genomics


title: 5Monocytes-Control

value: wt


title: ML2_CONTROL_R2

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR-2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode v28 release were used to obtain read counts at gene level considering only those reads aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Acute Myeloid Leukemia

growth_protocol: HL-60 and ML-2 cell lines were cultured in RPMI1640 medium supplemented with 20% fetal bovine serum (FBS) and maintained at 37°C in a humid atmosphere containing 5% CO2.

extract_protocol:
RNA was extracted with TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
MARS-seq; RNA from 0.1 x 106 cells from each experimental condition were purified using a Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific). For barcoded cDNA generation, polyadenylated RNA was retrotranscribed using an Affinity Script cDNA Synthesis Kit (Agilent Technologies), and barcoded primers also harboring T7 promoter and a partial Read2 sequence for illumine sequencing (CGATTGAGGCCGGTAATACGACTCACTATAGGGGGCGACGTGTGCTCTTCCGATCTXXXXXXNNNNTTTTTTTTTTTTTTTTTTTT, where XXXXXX is the cell barcode and NNN is a unique molecular identifier or UMI, which represents the same initial RNA molecule for future quantification). At this point, the samples were pooled (≤6 samples per pool) at equimolar ratios assessed by q-PCR. The samples were then treated with Exonuclease I (Thermo Fisher Scientific following a 1.2x positive SPRI-selection. Second-strand cDNA synthesis was then performed using a NEBNext Ultra II Directional RNA Second-Strand Synthesis Module (New England Biolabs) for 2 hours at 16ºC, followed by a 1.4x positive solid-phase   reverse immobilization (SPRI) cleanup. The samples were linearly amplified by T7 in vitro transcription using a T7 RNA Polymerase (New England Biolabs) for 16 hours at 37ºC. After DNAse treatment (TURBO DNAse I, Thermo Fisher Scientific) for 15 minutes at 37ºC to remove dsDNA, samples were cleaned with a positive 1.2x SPRI-selection. RNA size, quality, and concentration were determined by analysis with a Qubit Fluorometer (Termo Fisher Scientific) and TapeStation (Agilent 4200 TapeSation System, Agilent Technologies). If necessary, RNA was fragmented in 200- to 300-bp fragments using Zn2+divalent cations followed by a 2x positive SPRI cleanup. Fragmented RNA was dephosphorylated using FastAP Thermosensitive Alkaline Phosphatase (Thermo Fisher Scientific) for 10 minutes at 37ºC to enhance RNA ligation yield. In this step, a partial Read1 (AGATCGGAAGAGCGTCGTGTAG) sequence for illumine sequencing was ligated to the 3′ end of the fragmented RNA using T4 RNA Ligase I (New England Biolabs). After a 1.5x positive SPRI cleanup, the RNA product was retrotranscribed using an Affinity Script cDNA Synthesis Kit (Agilent Technologies) and a specific retrotranscription primer (TCTAGCCTTCTCGCAGCACATC). The library was then purified by 1.5x positive SPRI cleanup, and the yield of the previous steps was determined by q-PCR. Finally, PCR using KAPA HiFi HotStar Ready Mix (Kapa Biosystems) was performed for second-strand cDNA synthesis, illumine primers addition (Read1-P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCT CTTCCGATCT and Read2-P7: CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT) and library amplification using the recommended cycle numbers to minimize over-amplification. The product was purified by a 0.7x positive SPRI cleanup. The quality of the final library was determined by q-PCR (based on the threshold cycle, or Ct, obtained for GAPDH (Fw: CCAGCAAGAGCACAAGAGGAA, Rv: GATTCAGTGTGGTGGGGG) or GUSB (Fw: CAAGTGCCTCCTGGACTGTT, Rv: TCCACCTTTAGTGTTCCCTGC) housekeeping genes calibrated per individual set of samples, Qubit Fluorometer (Thermo Fisher Scientific) and TapeStation (Agilent 4200 TapeStation System, Agilent Technologies)l All libraries were pooled at equimolar ratios and sequenced on a NextSeq500 (Illumina) using 60 bp single-end reads at a minimum sequence depth of 10 million reads per sample.

treatment_protocol: HL-60 and ML-2 cells were treated with CM-444, CM-1758, Panobinostat and Vorinostat for 12hours.

value: Acute Myeloid Leukemia

value: myeloblast

value: Untreated


title: 4Monocytes-BCG

value: BCG


title: ML2_CONTROL_R3


title: L3 48h Flu

description: 10x Genomics


title: L3 72h SARS LMO

description: 10x Genomics

value: SARS/NT


title: 3Monocytes-Control


title: ML2_CM444_12H_R3


title: 2Monocytes-BCG


title: ML2_CONTROL_R1


title: L3 72h SARS

description: 10x Genomics


title: L3 48h SARS LMO

description: 10x Genomics


title: CBMC_PBS_2

value: Cord Blood

value: Mast cell


title: ML2_CM444_12H_R2


title: 6Neutrophils-BCG

value: Neutrophils (CD45+CD11b+Ly6G+)


title: UKN1_SBAD2_Ethylparaben_316_1


title: L3 48h SARS

description: 10x Genomics


title: UKN1_SBAD2_Ethylparaben_316_2


title: UKN1_SBAD2_Ethylparaben_100_1


title: UKN1_SBAD2_Ethylparaben_31.6_3


title: WD39_iPast (healthy)

city: Tokyo

first: Nicolas

last: Leventoux

address: 35, Shinanomachi

department: Physiology

institute: Keio University

data_processing:
Libraries were sequenced using a NovaSeq6000 (Illumina) to obtain 150-bp paired-end reads.
Fastp (version 0.23.2) was used for raw fastq quality control and adapter trimming.
Quantification of number of reads were performed using Salmon (version 1.6).
Salmon output files were converted using tximport (version 1.22.0).
tximport files were normalized by vst transformation using DESeq2 (version 1.34.0) for group comparisons.
Reads were aligned to the GRCh38.p13 reference genome (release 42).
Assembly: GRCh38.p13 reference genome (release 42)
Supplementary files format and content: featurecounts.xlsx: Excel file includes count data prior to normalization and includes 201B7_iPast and WD39_iPast, 2 control iPasts accessible on NCBI GEO under number GSE161024 as newly aligned to the GRCh38.p13 reference genome.
Supplementary files format and content: quant.sf: Salmon output files for the Kii ALS/PDC iPasts.

source_name: astrocytes (iPasts)

growth_protocol: iPast grew in MHM + B27 + NEAA + BDNF and GDNF.

extract_protocol:
We extracted RNA using the RNeasy kit (QIAGEN) according to manufacturer's protocol.
The indexed cDNA libraries were prepared using the Nextera XT library preparation kit (Illumina)

value: astrocytes (iPasts)

tag: disease

value: healthy


title: UKN1_SBAD2_Ethylparaben_31.6_2

value: SBAD2 iPS cells

value: male


title: 5Neutrophils-Control

value: Bone Marrow

value: immune cells


title: ML2_CM444_12H_R1


title: ML2_CM1758_12H_R3


title: 201B7_iPast (healthy)


title: UKN1_SBAD2_Ethylparaben_100_3


title: UKN1_SBAD2_Ethylparaben_100_2


title: Kii6-iPast

data_processing:
RNA was amplified using a SMART-Seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio).
Fastp (version 0.23.2) was used for raw fastq quality control and adapter trimming.
Quantification of number of reads were performed using Salmon (version 1.6).
Salmon output files were converted using tximport (version 1.22.0).
tximport files were normalized by vst transformation using DESeq2 (version 1.34.0) for group comparisons.
Reads were aligned to the GRCh38.p13 reference genome (release 42).
Assembly: GRCh38.p13 reference genome (release 42)
Supplementary files format and content: featurecounts.xlsx: Excel file includes count data prior to normalization and includes 201B7_iPast and WD39_iPast, 2 control iPasts accessible on NCBI GEO under number GSE161024 as newly aligned to the GRCh38.p13 reference genome.
Supplementary files format and content: quant.sf: Salmon output files for the Kii ALS/PDC iPasts.

growth_protocol: Astrocytes were maintained in MHM containing 2% B27, 0.8% NEAA and 10mg/mL of BDNF and GDNF.

extract_protocol:
We extracted RNA using the RNeasy kit (QIAGEN) according to manufacturer's protocol.
Library was created using a Nextera XT DNA library prep kit (Illumina).

value: Kii ALS/PDC


title: 4Neutrophils-BCG


title: 3Neutrophils-Control

value: PBS


title: UKN1_SBAD2_Ethylparaben_31.6_1

data_processing: All analyses were conducted using the statistical software R, version 4.2.1 Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.


title: ML2_CM1758_12H_R2


title: Kii4-iPast


title: ML2_CM1758_12H_R1


title: 2Neutrophils-BCG

value: wt


title: 6NK-BCG

source_name: Spleen

value: Spleen

value: NK cells (CD45+CD11-Nk1.1+)


title: 1Neutrophils-Control


title: ML2_CM124_12H_R2

value: Acute Myeloid Leukemia

value: myeloblast

value: Panobinostat


title: Kii2-iPast


title: UKN1_SBAD2_Ethylparaben_10_3


title: Kii1-iPast


title: Kii3-iPast


title: ML2_CM124_12H_R1


title: 5NK-Control


title: UKN1_SBAD2_Ethylparaben_10_4


title: UKN1_SBAD2_Ethylparaben_31.6_4


title: ML2_CM24_12H_R3

value: Vorinostat


title: UKN1_SBAD2_Ethylparaben_10_2


title: 4NK-BCG

value: BCG


title: CSF, HC 12

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

data_processing:
Demultiplexing with cellranger v6.0 mkfastq
Barcode and UMI deconvolution, mapping with cellranger v6 count
Assembly: GRCh38
Supplementary files format and content: .h5 files (HDF5) for cellranger of deconvoluted gene expression matrix

source_name: CSF

extract_protocol:
NA
10X Gene Expression

value: CSF

value: multiple

value: healthy control

tag: condition


title: 3NK-Control


title: CSF, PASC-CI, persistent 6

value: SARS CoV 2

value: PASC-CI, persistent


title: ML2_CM124_12H_R3


title: 2NK-BCG


title: ML2_CM24_12H_R1


title: ML2_CM24_12H_R2


title: UKN1_SBAD2_Ethylparaben_3.16_3

first: Jan

address: Ardeystraße 67

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

extract_protocol: Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).

value: SBAD2 iPS cells

value: male


title: UKN1_SBAD2_Ethylparaben_3.16_2


title: UKN1_SBAD2_Ethylparaben_3.16_4


title: HL60_CONTROL_R3

value: Untreated


title: 1NK-Control

value: immune cells

value: PBS


title: UKN1_SBAD2_Ethylparaben_3.16_1


title: UKN1_SBAD2_Ethylparaben_1_4


title: UKN1_SBAD2_Ethylparaben_10_1


title: 1Monocytes-Control

value: Bone Marrow

value: Monocytes (CD45+CD11b+Ly6C+)

value: wt


title: CSF, HC 11


title: HL60_CONTROL_R2

value: Acute Myeloid Leukemia

value: myeloblast


title: CSF, PASC-CI, persistent 5


title: UKN1_SBAD2_Ethylparaben_1_2


title: HL60_CONTROL_R1


title: CSF, HC 10


title: HL60_CM444_12H_R3


title: CSF, PASC-SCC 4

value: PASC-SCC


title: Replicate 3, scRNA-seq

city: Chicago

first: Bana

last: Jabri

state: Illinois

address: 900 E 57th Street

department: Department of Medicine

institute: University of Chicago

description: 10X Genomics

data_processing:
Sample-specific spliced count matrices were obtained using the "count" command from CellRanger (version 6.1.2).
Sample-specific spliced and unspliced counts were determined using the "run10x" command from the Velocyto software (version 0.7.17)
Assembly: mm10
Supplementary files format and content: Tab-separated values, matrix, and loom files

source_name: Bone marrow

extract_protocol:
Femur, tibia, and ilium bones were harvested, cut open and crushed. Bone marrow cells were then passed through a 70-µm cell strainer and resuspended in FACS buffer.
GEM RT Incubation, Post GEM-RT Cleanup, cDNA amplification, and Gene Expression Library Construction were performed as described in the Single Cell 3’ Reagent Kits User Guide v3.1 RevD (10X Genomics). Prior to sequencing, the three single-cell libraries were quantified using the KAPA Library Quantification Kit for Illumina Platforms (Roche, 501965234) and pooled in an equimolar ratio.

value: Bone marrow

value: Innate lymphocytes and innate lymphocyte progenitors


title: CSF, PASC-CI, improved 5

value: CSF

value: multiple

value: PASC-CI, improved


title: Replicate 2, scRNA-seq

description: 10X Genomics


title: Replicate 1, scRNA-seq

description: 10X Genomics


title: CSF, PASC-CI, persistent 4

value: SARS CoV 2

value: PASC-CI, persistent


title: M_C4877, K14-CreERT;ABCA12-cKO (KA) sample 4, female

city: Ann Arbor

first: Sunny

last: Wong

state: MI

address: 3217 Cancer Center

department: Dermatology

institute: University of Michigan

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR, v2.6.1d) software
FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene.
Differential expression analysis between two conditions/groups (3-4 biological replicates per condition) was performed using DESeq2 (1.40.2) R package.
Assembly: mm10
Supplementary files format and content: Comma-separated values file summarize raw counts, and analyzed data from DESeq2 of each samples.

source_name: epidermis from telogen skin

growth_protocol: 8 week old mice were injected intraperitoneally with tamoxifen dissolved in corn oil, at a dose of 1 mg/40 grams body weight for 3 consecutive days.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: The epidermis was isolated from telogen skin from KA mice or controls, 2 weeks post-TAM.

value: epidermis from telogen skin

value: 2 weeks post-Tamoxifen treatment


title: CSF, PASC-CI, persistent 3


title: UKN1_SBAD2_Ethylparaben_1_3

city: Dortmund

last: Hengstler

value: SBAD2 iPS cells

value: male


title: HL60_CM444_12H_R1


title: UKN1_SBAD2_Ethylparaben_0.316_3


title: CSF, HC 9

value: healthy control


title: HL60_CM24_12H_R3

value: Vorinostat


title: M_B4854, K14-CreERT;ABCA12-cKO (KA) sample 2, male


title: UKN1_SBAD2_Ethylparaben_1_1


title: M_C4876, K14-CreERT;ABCA12-cKO (KA) sample 3, female


title: CSF, HC 8


title: UKN1_SBAD2_Ethylparaben_0.316_2


title: UKN1_SBAD2_Butylparaben_31.6_3


title: M_A4855, K14-CreERT;ABCA12-cKO (KA) sample 1, male


title: C_C4875, control sample 3 (no CreERT), female


title: CSF, PASC-SCC 3


title: HL60_CM444_12H_R2


title: HL60_CM24_12H_R1


title: C_B4853 ,control sample 2 (no CreERT), male


title: CSF, HC 7


title: CSF, HC 6


title: HL60_CM1758_12H_R2


title: C_A4857, control sample 1 (no CreERT), female


title: HL60_CM24_12H_R2


title: CSF, HC 5


title: HL60_CM1758_12H_R1


title: CSF, PASC-CI, improved 4


title: neural stem cells, shMina53-rep2

city: Hangzhou

first: Jie

last: Sun

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
The raw sequence data were firstly quality trimmed by fatsp software to obtain the clean reads.
Then the clean reads were aligned to the Mus musculus reference genome mm39 using Bowtie2 and subsequently analyzed by the SEACR software based the ‘stringent’ parameter to detect genomic regions enriched for multiple overlapping DNA fragments (peaks).
Visualization of peak distribution along genomic regions was performed with Integrative Genomics Viewer (IGV)
Peak distribution and annotation were generated by ChIPseeker.
Different peaks between case and control groups were analyzed using Manorm software, the significantly different peaks were identified as p<0.05 and |log2(foldchange)|＞1.
Assembly: mm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: neural stem cells

extract_protocol:
Briefly, concanavalin A-coated magnetic beads (ConA beads) were used to bound cells. Non-ionic detergent Digitonin was used to permeate cell membrane. Then, H4R3me2a antibody (Cat#39705, Active motif) , secondary antibody and the Hyperactive pA-Tn5 Transposase were incubated with the cells that were bounded by ConA beads in order.
CUT&Tag assay was performed using HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (cat.no.TD901-TD902, Vazyme Biotech, China) according to manufacturer's instruction

value: neural stem cells

tag: chip antibody

value: H4R3me2a (Cat#39705, Active motif)


title: CSF, PASC_CI

value: PASC-CI


title: neural stem cells, shMina53-rep1


title: HL60_CM124_12H_R2

value: Acute Myeloid Leukemia

value: myeloblast

value: Panobinostat


title: HL60_CM1758_12H_R3


title: neural stem cells, scramble-rep2


title: HL60_CM124_12H_R3


title: UKN1_SBAD2_Butylparaben_31.6_1


title: neural stem cells, scramble-rep1


title: CSF, PASC-CI, persistent 2

value: CSF


title: UKN1_SBAD2_Butylparaben_10_3


title: ER19-post

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Data were aligned to mm10 genome and filtered for low abundance transcripts by keeping only genes expressed at CPM ≥5 in at least 85% of samples before further analysis.
After filtering, pair-wise differential expression comparisons using DEseq2 were performed to identify differentially expressed genes (DEGs) in comparisons of pre- and post-resilient vs control and susceptible vs control and a nominal significance threshold of fold change>2 and p<0.025 was applied.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Sperm

extract_protocol:
Total RNA was isolated from frozen mature sperm from adult male mice using a protocol combining TRIzol/chloroform extraction with RNeasy MiniElute Cleanup kit. In short, 200 µl Trizol was used to homogenize the tissue. An additional 500 µl Trizol was added along with 140 µl chloroform. The lysate was centrifuged at 12,000xg for 15 minutes and the aqueous layer was removed and added to the RNeasy mini spin column. The rest of the protocol was completed as outlined by the manufacturer. Samples were treated with DNAse to rid samples of genomic DNA. After extraction, purity and concentration were measured on an Agilent 2100 Bioanalyzer (Agilent, Santa Clara CA) using an RNA 6000 Nano assay.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold protocol (Illumina, San Diego, CA). Briefly, cDNA was synthesized from ribo-depleted RNA, followed by end-repair and ligation with sequencing adaptors. The libraries were then size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (8 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing. All libraries were pooled for multiplexing and sequenced on the Illumina HiSeq 2500 System utilizing V3 chemistry with 150 base pair double-end reads at the sequenced on a HighSeq2500 System using V4 chemistry with 50 base pair single-end reads at GeneWiz LLC (South Plainfield, NJ).

tag: surgery group

value: Control

value: Defeat

tag: si group

value: Susceptible

tag: sperm time point

value: Sperm


title: neural stem cells, shMina53 rep3

description: Sample 6

data_processing:
Illumina Casava 1.7software used for basecalling.
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Mina53 knockdown

value: proliferation


title: CSF, HC 4

tag: tissue

value: multiple


title: UKN1_SBAD2_Butylparaben_31.6_2

value: SBAD2 iPS cells

value: male


title: CSF, HC 3

tag: infection

value: healthy control


title: UKN1_SBAD2_Ethylparaben_0.316_1


title: neural stem cells, shMina53 rep2

description: Sample 5

value: neural stem cells


title: UKN1_SBAD2_Butylparaben_10_4


title: D33-post


title: UKN1_SBAD2_Butylparaben_10_1


title: neural stem cells, shMina53 rep1

description: Sample 4


title: HL60_CM124_12H_R1

tag: cell line


title: UKN1_SBAD2_Butylparaben_10_2


title: D37-post


title: neural stem cells, shcontrol rep3

description: Sample 3

tag: genotype

value: WT


title: AMC-ER20

tag: treatment


title: UKN1_SBAD2_Butylparaben_3.16_3

tag: cell type


title: CSF, HC 2


title: neural stem cells, shcontrol rep2

description: Sample 2


title: UKN1_SBAD2_Butylparaben_3.16_1


title: AMC-98-post


title: neural stem cells, shcontrol rep1

description: Sample 1


title: CSF, PASC-SCC 2

value: SARS CoV 2

value: PASC-SCC


title: CSF, PASC-CI, improved 3

value: PASC-CI, improved


title: AMC-96-post


title: CSF, PASC-CI, persistent 1

value: PASC-CI, persistent


title: AMC-93-post


title: CSF, HC 1

value: CSF


title: UKN1_SBAD2_Butylparaben_1_4


title: AMC-92-post

value: Control


title: UKN1_SBAD2_Butylparaben_3.16_4


title: CSF, PASC-CI, improved 1


title: AMC-91-post


title: CSF, PASC-SCC 1

value: T cells, myeloid cells


title: AMC-89-post

value: Defeat

value: Susceptible


title: Lymph node tissue of patient 8 (Spatial transcriptome)

city: Nanning

first: Wenyu

last: Feng

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

data_processing:
Processed data details to be added at a later date.
Library strategy: Spatial Transcriptomics

source_name: Lymph node tissue

extract_protocol:
Immediately after surgical excision to remove the tumor, we collected fresh samples and placed them in an ice solution containing Hank's balanced salt solution and 1% antifungal antibody, and transferred the tissue into a 4 ℃refrigerator for storage within 20 minutes. Subsequently, a small soft tissue sample was taken and cut into 1 mm3 pieces, washed well using DPBS (cat. no. C14190500BT; Thermo Fisher Scientific, Inc.), and digested by adding collagenase 2 (1 mg/mL) for 45 min at 37 ℃. The cells were filtered using a 100 uM cell filter, and the obtained cell suspension was centrifuged for 5 min at 300 g. The supernatant was removed, and red blood cells were removed using 1× red blood cell lysis buffer (10× diluted to 1×; cat. no. B250015; BioLegend, Inc.). Finally, after washing the cells with PBS, the cells were resuspended using BPBS. Meanwhile, cell viability will be assessed using 0.4% Trypan blue staining.
Paracancerous tissues contain more hard bone composition, which presents great challenges in single-cell sequencing. To overcome this limitation, in this study, we first used αMEM (SH30265.01, HyClone) to clean the hard bone three times and bite them into small pieces of about 1-2 mm in diameter. 12 ml of collagenase type II at a concentration of 2 mg/ml (Cat: A004174-0001, Sangon Biotech) was mixed with αMEM containing 100 U/ml penicillin and 100 μg/ml streptomycin (Cat:15140-122, Gibco) in a 50 ml conical tube. The bone snap was then placed in it and digested at 37 °C for 25 min with gentle agitation. Afterwards, the collagenase solution was removed aseptically and the bone pieces were rinsed three times in 10 ml of PBS. After five rounds of digestion, the collagenase solutions from the last two rounds of digestion were combined and the solutions were filtered through a 40 μm filter. Finally, Red Blood Cell Lysis Solution (10×) was used to remove red blood cells according to the manufacturer's instructions.
The final single cells from each sample were loaded on a 10× Genomics Chromium Single-Cell Chip along with the single cell master mix and single cell 3’ gel beads (10× Genomics) to generate single-cell gel bead-in-emulsions (GEMs). According to the manufacturer’s instructions the samples were processed by 10× Genomics V3 barcoding chemistry kits. mRNA in drops were undergo the reverse transcription reactions and then the cDNA amplification was followed by the instructions. And the single cell libraries were sequenced on an Illumina NovaSeq 6000 instrument.

tag: subject

value: patient 8

value: Lymph node tissue


title: Tumor adjacent tissue of patient 10

data_processing: Processed data details to be added at a later date.

source_name: Tumor adjacent tissue

value: patient 10

value: Tumor adjacent tissue


title: UKN1_SBAD2_Butylparaben_0.316_4

value: SBAD2 iPS cells

value: male


title: spontaneous miscarriage [ESC65]

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description: miRNA expression data from spontaneous miscarriage(Blighted ovum)

hyb_protocol: Standard Applied Biosystems FlashTag Biotin HSR RNA Labeling Kits protocol

data_processing: Normalize with Experssion(Gene) RMA+DABG (Human Only) by Applied Biosystems Transcriptome Analysis Console Ver 4.0

source_name: spontaneous miscarriage

growth_protocol: human decidual stromal cells were isolated from the decidual tissue(normal pregnancy and spontaneous miscarriage ).

extract_protocol: Exosomes used for RNA extraction were resuspended inTRI Reagent LS and protocol as detailed by manufacturer.

treatment_protocol: Extracellular vesicles were extracted from human decidual stromal cells  in media with FBS depleted of extracellular vesicles .

tag: subject status

value: spontaneous miscarriage

value: human decidaul stromal cells

value: primary cells


title: AMC-88-post

value: Resilient

value: Sperm


title: CSF, PASC-CI, improved 2

value: multiple

value: SARS CoV 2

value: PASC-CI, improved


title: normal pregancy  [ESC67]

description: miRNA expression data from noraml pregnancy

scan_protocol: Standard Applied Biosystems FlashTag Biotin HSR RNA Labeling Kits protocol

source_name: normal pregancy

value: normal pregancy